# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:50:24 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R,3S,5R)-2-(2,5-difluorophenyl)-5-(7H-pyrrolo[3',4':3,4]pyrazolo[1,5-a]pyrimidin-8(9H)-yl)oxan-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@H](CO[C@@H]1c2cc(F)ccc2F)N3Cc4nn5cccnc5c4C3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 6DG  6DG  (2R,3S,5R)-2-(2,5-difluorophenyl)-5-(7H-pyrrolo[3',4':3,4]pyrazolo[1,5-a]pyrimidin-8(9H)-yl)oxan-3-amine  ligand  46  27  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6DG
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 6DG  C2   C  CR16  0  -0.390   6.4272   0.2708  -0.6334
 6DG  C3   C  CR16  0  -0.441   4.3287  -1.1739   0.4739
 6DG  C5   C  CH2   0  -0.311  -2.2824   1.2438   0.7724
 6DG  C6   C  CH2   0  -0.470   0.5805   1.4205   0.4294
 6DG  C8   C  CR16  0  -0.403  -7.7768  -0.5798  -0.0442
 6DG  C9   C  CR16  0   0.083  -7.0581   0.4155   0.5417
 6DG  F27  F  F     0  -0.309   4.8736   1.6958  -1.6443
 6DG  C12  C  CR6   0   0.500   5.1114   0.6268  -0.8635
 6DG  C13  C  CR6   0  -0.098   4.0400  -0.0709  -0.3277
 6DG  C11  C  CR6   0   0.538   5.6411  -1.5289   0.7042
 6DG  F26  F  F     0  -0.316   5.8952  -2.5970   1.4778
 6DG  C1   C  CR16  0  -0.404   6.7025  -0.8277   0.1644
 6DG  C19  C  CH1   0   0.013   2.6132   0.3496  -0.5537
 6DG  C18  C  CH1   0  -0.111   2.0626   1.1391   0.6516
 6DG  N20  N  NH2   0  -0.789   2.7581   2.3787   0.9250
 6DG  O25  O  O2    0  -0.490   1.8556  -0.8192  -0.7710
 6DG  C7   C  CH2   0  -0.181   0.5006  -0.5549  -1.0529
 6DG  C17  C  CH1   0  -0.065  -0.1897   0.1404   0.1181
 6DG  N24  N  NR5   0  -0.474  -1.5712   0.4183  -0.2156
 6DG  C4   C  CH2   0  -0.341  -2.3654  -0.7820  -0.5477
 6DG  C15  C  CR55  0   0.253  -3.6895   0.8176   0.5582
 6DG  N21  N  N     0  -0.333  -4.8680   1.2775   0.9416
 6DG  N23  N  N     0  -0.362  -5.7160   0.3802   0.4242
 6DG  C16  C  CR56  0   0.523  -5.0790  -0.6467  -0.2859
 6DG  C14  C  CR55  0  -0.189  -3.7376  -0.3428  -0.1918
 6DG  N22  N  N     0  -0.424  -5.7819  -1.6302  -0.8668
 6DG  C10  C  CR16  0  -0.053  -7.0815  -1.5927  -0.7455
 6DG  H1   H  HCR6  0   0.291   7.2301   0.8454  -1.0754
 6DG  H2   H  HCR6  0   0.285   3.5304  -1.7554   0.9169
 6DG  H4   H  HCH2  0   0.260  -2.1178   2.3090   0.5973
 6DG  H5   H  HCH2  0   0.258   0.1884   1.9123   1.3221
 6DG  H6   H  HCH2  0   0.227   0.4585   2.1207  -0.4066
 6DG  H7   H  HCR6  0   0.293  -8.8531  -0.5920   0.0283
 6DG  H8   H  HCR6  0   0.324  -7.4817   1.2380   1.0994
 6DG  H9   H  HCR6  0   0.291   7.7231  -1.1283   0.3587
 6DG  H10  H  HCH1  0   0.230   2.5500   1.0032  -1.4379
 6DG  H11  H  HCH1  0   0.240   2.1622   0.4991   1.5361
 6DG  H12  H  HNH2  0   0.354   3.7257   2.2071   1.1668
 6DG  H13  H  HNH2  0   0.342   2.7590   2.9729   0.1046
 6DG  H15  H  HCH2  0   0.205   0.4041   0.0773  -1.9482
 6DG  H16  H  HCH2  0   0.251   0.0446  -1.5205  -1.2754
 6DG  H17  H  HCH1  0   0.206  -0.1252  -0.5262   0.9988
 6DG  H18  H  HCH2  0   0.251  -2.2476  -1.0471  -1.6011
 6DG  H19  H  HCR6  0   0.275  -7.6402  -2.3928  -1.2168
 6DG  H14  H  HCH2  0   0.224  -2.0619  -1.6615   0.0420
 6DG  H3   H  HCH2  0   0.236  -1.9781   1.0324   1.8094

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 6DG  N20  C18  single    1.447  0.020  1.447
 6DG  C18  C6   single    1.525  0.020  1.525
 6DG  C18  C19  single    1.542  0.020  1.542
 6DG  F26  C11  single    1.343  0.020  1.343
 6DG  C6   C17  single    1.526  0.020  1.526
 6DG  C11  C1   aromatic  1.382  0.020  1.382
 6DG  C11  C3   aromatic  1.379  0.020  1.379
 6DG  C5   C15  single    1.486  0.020  1.486
 6DG  C5   N24  single    1.471  0.020  1.471
 6DG  C1   C2   aromatic  1.385  0.020  1.385
 6DG  C3   C13  aromatic  1.394  0.020  1.394
 6DG  N21  C15  aromatic  1.322  0.020  1.322
 6DG  N21  N23  aromatic  1.339  0.020  1.339
 6DG  C2   C12  aromatic  1.382  0.020  1.382
 6DG  C15  C14  aromatic  1.382  0.020  1.382
 6DG  C13  C12  aromatic  1.386  0.020  1.386
 6DG  C13  C19  single    1.505  0.020  1.505
 6DG  C17  N24  single    1.448  0.020  1.448
 6DG  C17  C7   single    1.527  0.020  1.527
 6DG  C12  F27  single    1.345  0.020  1.345
 6DG  C19  O25  single    1.410  0.020  1.410
 6DG  N24  C4   single    1.477  0.020  1.477
 6DG  N23  C9   aromatic  1.348  0.020  1.348
 6DG  N23  C16  aromatic  1.402  0.020  1.402
 6DG  C9   C8   aromatic  1.360  0.020  1.360
 6DG  O25  C7   single    1.409  0.020  1.409
 6DG  C14  C4   single    1.484  0.020  1.484
 6DG  C14  C16  aromatic  1.379  0.020  1.379
 6DG  C16  N22  aromatic  1.341  0.020  1.341
 6DG  C8   C10  aromatic  1.415  0.020  1.415
 6DG  N22  C10  aromatic  1.306  0.020  1.306
 6DG  C2   H1   single    0.930  0.020  1.080
 6DG  C3   H2   single    0.930  0.020  1.080
 6DG  C5   H3   single    0.970  0.020  1.090
 6DG  C5   H4   single    0.970  0.020  1.090
 6DG  C6   H5   single    0.970  0.020  1.090
 6DG  C6   H6   single    0.970  0.020  1.090
 6DG  C8   H7   single    0.930  0.020  1.080
 6DG  C9   H8   single    0.930  0.020  1.080
 6DG  C1   H9   single    0.930  0.020  1.080
 6DG  C19  H10  single    0.970  0.020  1.090
 6DG  C18  H11  single    0.970  0.020  1.090
 6DG  N20  H12  single    0.890  0.020  1.040
 6DG  N20  H13  single    0.890  0.020  1.040
 6DG  C7   H15  single    0.970  0.020  1.090
 6DG  C7   H16  single    0.970  0.020  1.090
 6DG  C17  H17  single    0.970  0.020  1.090
 6DG  C4   H18  single    0.970  0.020  1.090
 6DG  C10  H19  single    0.930  0.020  1.080
 6DG  C4   H14  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 6DG  H1   C2   C1   120.60  3.000
 6DG  H1   C2   C12  120.11  3.000
 6DG  C1   C2   C12  119.29  3.000
 6DG  H2   C3   C11  119.69  3.000
 6DG  H2   C3   C13  120.52  3.000
 6DG  C11  C3   C13  119.80  3.000
 6DG  H4   C5   H3   107.25  3.000
 6DG  H4   C5   C15  113.54  3.000
 6DG  H3   C5   C15  110.03  3.000
 6DG  H4   C5   N24  111.52  3.000
 6DG  H3   C5   N24  113.03  3.000
 6DG  C15  C5   N24  101.54  3.000
 6DG  H6   C6   H5   107.19  3.000
 6DG  H6   C6   C17  108.89  3.000
 6DG  H5   C6   C17  111.30  3.000
 6DG  H6   C6   C18  109.68  3.000
 6DG  H5   C6   C18  108.24  3.000
 6DG  C17  C6   C18  111.43  3.000
 6DG  H7   C8   C10  121.03  3.000
 6DG  H7   C8   C9   120.43  3.000
 6DG  C10  C8   C9   118.54  3.000
 6DG  H8   C9   N23  117.09  3.000
 6DG  H8   C9   C8   124.91  3.000
 6DG  N23  C9   C8   118.00  3.000
 6DG  C13  C12  F27  119.19  3.000
 6DG  F27  C12  C2   118.01  3.000
 6DG  C13  C12  C2   122.80  3.000
 6DG  C19  C13  C12  122.29  3.000
 6DG  C19  C13  C3   120.26  3.000
 6DG  C12  C13  C3   117.42  3.000
 6DG  C1   C11  F26  118.89  3.000
 6DG  C1   C11  C3   122.36  3.000
 6DG  F26  C11  C3   118.75  3.000
 6DG  H9   C1   C11  120.90  3.000
 6DG  H9   C1   C2   120.76  3.000
 6DG  C11  C1   C2   118.34  3.000
 6DG  H10  C19  O25  109.72  3.000
 6DG  H10  C19  C18  107.64  3.000
 6DG  O25  C19  C18  110.67  3.000
 6DG  H10  C19  C13  109.93  3.000
 6DG  O25  C19  C13  107.52  3.000
 6DG  C18  C19  C13  111.36  3.000
 6DG  H11  C18  N20  107.69  3.000
 6DG  H11  C18  C19  107.41  3.000
 6DG  N20  C18  C19  114.48  3.000
 6DG  H11  C18  C6   108.28  3.000
 6DG  C19  C18  C6   109.12  3.000
 6DG  N20  C18  C6   109.66  3.000
 6DG  H13  N20  H12  106.98  3.000
 6DG  H13  N20  C18  110.47  3.000
 6DG  H12  N20  C18  111.06  3.000
 6DG  C7   O25  C19  113.09  3.000
 6DG  H16  C7   H15  107.82  3.000
 6DG  H16  C7   C17  111.75  3.000
 6DG  H15  C7   C17  108.83  3.000
 6DG  H16  C7   O25  106.07  3.000
 6DG  H15  C7   O25  110.79  3.000
 6DG  C17  C7   O25  111.51  3.000
 6DG  H17  C17  N24  110.77  3.000
 6DG  H17  C17  C7   108.04  3.000
 6DG  N24  C17  C7   110.00  3.000
 6DG  H17  C17  C6   108.28  3.000
 6DG  C7   C17  C6   108.08  3.000
 6DG  N24  C17  C6   111.56  3.000
 6DG  C4   N24  C17  114.13  3.000
 6DG  C4   N24  C5   110.31  3.000
 6DG  C17  N24  C5   114.47  3.000
 6DG  H14  C4   H18  107.02  3.000
 6DG  H14  C4   C14  111.27  3.000
 6DG  H18  C4   C14  113.74  3.000
 6DG  H14  C4   N24  112.36  3.000
 6DG  H18  C4   N24  110.85  3.000
 6DG  C14  C4   N24  101.69  3.000
 6DG  C14  C15  N21  114.73  3.000
 6DG  C14  C15  C5   110.60  3.000
 6DG  N21  C15  C5   134.65  3.000
 6DG  N23  N21  C15  102.68  3.000
 6DG  C16  N23  N21  113.52  3.000
 6DG  C16  N23  C9   121.06  3.000
 6DG  N21  N23  C9   125.42  3.000
 6DG  N22  C16  C14  134.52  3.000
 6DG  N22  C16  N23  121.24  3.000
 6DG  C14  C16  N23  104.25  3.000
 6DG  C16  C14  C15  104.82  3.000
 6DG  C16  C14  C4   144.89  3.000
 6DG  C15  C14  C4   110.27  3.000
 6DG  C10  N22  C16  117.40  3.000
 6DG  H19  C10  N22  116.84  3.000
 6DG  H19  C10  C8   119.39  3.000
 6DG  N22  C10  C8   123.77  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 6DG  CONST_01  C3   C11  C1   C2      0.00   0.0  0
 6DG  CONST_02  C3   C13  C12  C2      0.00   0.0  0
 6DG  CONST_03  N21  N23  C9   C8    180.00   0.0  0
 6DG  CONST_04  C16  N23  C9   C8      0.00   0.0  0
 6DG  CONST_05  C16  N22  C10  C8      0.00   0.0  0
 6DG  CONST_06  C15  N21  N23  C9    180.00   0.0  0
 6DG  CONST_07  C14  C16  N23  C9    180.00   0.0  0
 6DG  CONST_08  N22  C16  N23  C9      0.00   0.0  0
 6DG  CONST_09  N22  C10  C8   C9      0.00   0.0  0
 6DG  CONST_10  C11  C1   C2   C12     0.00   0.0  0
 6DG  CONST_11  C11  C3   C13  C12     0.00   0.0  0
 6DG  CONST_12  C1   C11  C3   C13     0.00   0.0  0
 6DG  CONST_13  C1   C2   C12  C13     0.00   0.0  0
 6DG  CONST_14  C16  N23  N21  C15     0.00   0.0  0
 6DG  CONST_15  N23  C16  C14  C15     0.00   0.0  0
 6DG  CONST_16  N22  C16  C14  C15   180.00   0.0  0
 6DG  CONST_17  C16  C14  C15  N21     0.00   0.0  0
 6DG  CONST_18  C14  C16  N23  N21     0.00   0.0  0
 6DG  CONST_19  N22  C16  N23  N21   180.00   0.0  0
 6DG  CONST_20  C14  C15  N21  N23     0.00   0.0  0
 6DG  CONST_21  C10  C8   C9   N23     0.00   0.0  0
 6DG  CONST_22  C10  N22  C16  N23     0.00   0.0  0
 6DG  CONST_23  C10  N22  C16  C14   180.00   0.0  0
 6DG  CONST_24  C19  C13  C12  C2    180.00   0.0  0
 6DG  CONST_25  C19  C13  C3   C11   180.00   0.0  0
 6DG  CONST_26  F26  C11  C1   C2    180.00   0.0  0
 6DG  CONST_27  F27  C12  C13  C3    180.00   0.0  0
 6DG  CONST_28  C1   C2   C12  F27   180.00   0.0  0
 6DG  CONST_29  C19  C13  C12  F27     0.00   0.0  0
 6DG  CONST_30  F26  C11  C3   C13   180.00   0.0  0
 6DG  CONST_31  H9   C1   C11  C3    180.00   0.0  0
 6DG  CONST_32  H19  C10  C8   C9    180.00   0.0  0
 6DG  CONST_33  H2   C3   C13  C12   180.00   0.0  0
 6DG  CONST_34  H1   C2   C12  C13   180.00   0.0  0
 6DG  CONST_35  H8   C9   N23  N21     0.00   0.0  0
 6DG  CONST_36  H7   C8   C9   N23   180.00   0.0  0
 6DG  Var_01    C14  C4   N24  C5     23.12  30.0  1
 6DG  Var_02    C17  C7   O25  C19   -62.39  30.0  1
 6DG  Var_03    C15  C5   N24  C17  -153.60  30.0  1
 6DG  Var_04    N21  C15  C5   N24  -167.51  30.0  1
 6DG  Var_05    C15  C14  C4   N24   -13.58  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 6DG  chir_01  C19  C18  C13  O25  negativ
 6DG  chir_02  C18  N20  C19  C6   positiv
 6DG  chir_03  C17  N24  C7   C6   negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 6DG  plan-1  C2   0.020
 6DG  plan-1  C3   0.020
 6DG  plan-1  F27  0.020
 6DG  plan-1  C12  0.020
 6DG  plan-1  C13  0.020
 6DG  plan-1  C11  0.020
 6DG  plan-1  F26  0.020
 6DG  plan-1  C1   0.020
 6DG  plan-1  C19  0.020
 6DG  plan-1  H1   0.020
 6DG  plan-1  H2   0.020
 6DG  plan-1  H9   0.020
 6DG  plan-2  C5   0.020
 6DG  plan-2  C8   0.020
 6DG  plan-2  C9   0.020
 6DG  plan-2  C4   0.020
 6DG  plan-2  C15  0.020
 6DG  plan-2  N21  0.020
 6DG  plan-2  N23  0.020
 6DG  plan-2  C16  0.020
 6DG  plan-2  C14  0.020
 6DG  plan-2  N22  0.020
 6DG  plan-2  C10  0.020
 6DG  plan-2  H7   0.020
 6DG  plan-2  H8   0.020
 6DG  plan-2  H19  0.020

